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SignacX: Cell Type Identification and Discovery from Single Cell Gene Expression Data

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.

Version: 2.2.5
Depends: R (≥ 3.5.0)
Imports: neuralnet, lme4, methods, Matrix, pbmcapply, Seurat (≥ 3.2.0), RJSONIO, igraph (≥ 1.2.1), jsonlite (≥ 1.5), RColorBrewer (≥ 1.1.2), stats
Suggests: hdf5r, rhdf5, knitr, rmarkdown, formatR
Published: 2021-11-18
DOI: 10.32614/CRAN.package.SignacX
Author: Mathew Chamberlain [aut, cre], Virginia Savova [aut], Richa Hanamsagar [aut], Frank Nestle [aut], Emanuele de Rinaldis [aut], Sanofi US [fnd]
Maintainer: Mathew Chamberlain <chamberlainphd at gmail.com>
BugReports: https://github.com/mathewchamberlain/SignacX/issues
License: GPL-3
URL: https://github.com/mathewchamberlain/SignacX
NeedsCompilation: no
Citation: SignacX citation info
Materials: README NEWS
In views: Omics
CRAN checks: SignacX results

Documentation:

Reference manual: SignacX.pdf
Vignettes: Mapping homologous gene symbols
Benchmarking SignacX and SingleR with flow-sorted data
Analysis of Kidney lupus data from AMP
Analysis of CITE-seq PBMCs from 10X Genomics
Analysis of PBMCs from 10X Genomics
Mapping cells from CITE-seq PBMCs from 10X Genomics to another data set
Benchmarking SignacFast with flow-sorted data

Downloads:

Package source: SignacX_2.2.5.tar.gz
Windows binaries: r-devel: SignacX_2.2.5.zip, r-release: SignacX_2.2.5.zip, r-oldrel: SignacX_2.2.5.zip
macOS binaries: r-release (arm64): SignacX_2.2.5.tgz, r-oldrel (arm64): SignacX_2.2.5.tgz, r-release (x86_64): SignacX_2.2.5.tgz, r-oldrel (x86_64): SignacX_2.2.5.tgz
Old sources: SignacX archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=SignacX to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.